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OPENSEQ.org
L14-vs-TsaB
Genes: A B A+B
Length: 123 231 349
Sequences: 1778 3108 1342
Seq/Len: 14.46 13.45 3.85
MirrorTree (Pazo et al. 2001) 0.56
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.09 0.00 0.00
2 0.09 0.00 0.00
5 0.09 0.00 0.00
10 0.09 0.00 0.00
20 0.09 0.00 0.03
100 0.09 0.00 0.88
∞ 0.10 0.00 3.79
Paired alignment generation
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Sequence A E-value:
Iterations:
Sequence B E-value:
Iterations:
Δgene MSA
Figure 1: The effect of Δgene on ratio of paralogs in the genome for each gene, and the number of sequences in the resulting joined alignment. Figure 2: Distribution of Δgene across all genomes. Figure 3: Current parameters. You can use the form to adjust the parameters and resubmit the job!
GREMLIN results (Scaled_score > 1):
Figure 4: The darker and larger the blue dots, the higher strength in coevolution. 		Inter Residue pairs sorted by strength in coevolution signal:
i j Scaled Score Prob I_Prob
31_R 121_E 1.15 0.85 0.10
43_I 97_T 1.13 0.84 0.10
104_T 67_S 1.12 0.83 0.10
25_L 55_D 1.11 0.82 0.09
14_S 229_G 0.98 0.70 0.06
88_N 80_G 0.95 0.66 0.06
72_P 74_G 0.94 0.66 0.06
56_D 120_G 0.93 0.64 0.05
87_L 83_L 0.92 0.63 0.05
6_T 44_D 0.89 0.59 0.05
87_L 212_H 0.89 0.58 0.04
42_T 77_I 0.88 0.58 0.04
104_T 79_Q 0.87 0.56 0.04
56_D 93_S 0.87 0.56 0.04
14_S 101_G 0.85 0.54 0.04
84_C 194_M 0.84 0.52 0.04
93_Q 224_W 0.83 0.52 0.04
57_V 43_Q 0.83 0.51 0.04
72_P 173_L 0.83 0.51 0.04
57_V 93_S 0.82 0.50 0.04
35_V 109_T 0.82 0.50 0.04
88_N 16_A 0.82 0.50 0.04
66_K 229_G 0.81 0.49 0.04
88_N 14_S 0.81 0.48 0.03
90_N 80_G 0.80 0.47 0.03
14_S 93_S 0.80 0.47 0.03
83_A 114_A 0.79 0.46 0.03
86_L 211_E 0.79 0.46 0.03
78_R 209_A 0.79 0.46 0.03
33_A 37_R 0.79 0.45 0.03
93_Q 36_Q 0.78 0.45 0.03
77_I 15_V 0.77 0.42 0.03
86_L 17_L 0.76 0.42 0.03
43_I 196_P 0.76 0.42 0.03
6_T 82_A 0.76 0.42 0.03
38_I 5_A 0.75 0.41 0.03
99_I 39_L 0.75 0.40 0.03
35_V 49_S 0.74 0.40 0.03
57_V 214_E 0.74 0.40 0.03
116_I 63_R 0.74 0.39 0.03
55_G 70_G 0.74 0.39 0.03
42_T 52_S 0.73 0.39 0.03
35_V 57_N 0.73 0.39 0.03
83_A 119_M 0.73 0.39 0.03
59_K 42_V 0.73 0.38 0.03
69_V 189_P 0.72 0.37 0.03
99_I 97_T 0.72 0.36 0.02
18_R 119_M 0.72 0.36 0.02
17_R 101_G 0.71 0.35 0.02
32_Y 76_G 0.71 0.35 0.02
111_K 111_V 0.71 0.35 0.02
58_L 221_N 0.71 0.35 0.02
78_R 80_G 0.70 0.35 0.02
14_S 195_L 0.70 0.34 0.02
84_C 84_G 0.70 0.34 0.02
19_V 60_A 0.70 0.34 0.02
28_S 219_R 0.69 0.34 0.02
123_L 15_V 0.69 0.34 0.02
86_L 111_V 0.69 0.33 0.02
43_I 157_S 0.69 0.33 0.02
55_G 34_H 0.69 0.33 0.02
14_S 75_I 0.68 0.32 0.02
17_R 12_A 0.68 0.32 0.02
89_N 123_Y 0.68 0.32 0.02
2_I 91_G 0.68 0.32 0.02
110_E 203_A 0.68 0.32 0.02
99_I 12_A 0.67 0.31 0.02
72_P 85_A 0.67 0.31 0.02
6_T 228_P 0.67 0.31 0.02
54_K 213_A 0.67 0.31 0.02
34_G 121_E 0.67 0.31 0.02
84_C 89_M 0.67 0.30 0.02
95_I 163_V 0.67 0.30 0.02
6_T 148_I 0.66 0.30 0.02
81_G 230_K 0.66 0.30 0.02
18_R 218_L 0.66 0.30 0.02
47_I 35_T 0.66 0.29 0.02
83_A 90_I 0.66 0.29 0.02
18_R 61_Y 0.65 0.29 0.02
76_V 74_G 0.65 0.29 0.02
111_K 58_A 0.65 0.29 0.02
104_T 13_C 0.65 0.28 0.02
Figure 5: The i (protein A) and j (protein B) are positions as given in the query sequences.

Scaled Score = raw_score/average(raw_scores)
Prob = P(contact | scaled_score, seq/len)
I_Prob = P(contact | scaled_score, seq/len, top_inter_score)
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